Starting phenix.real_space_refine
on Thu Dec  7 18:28:29 2023 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u11_26274/12_2023/7u11_26274.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u11_26274/12_2023/7u11_26274.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u11_26274/12_2023/7u11_26274.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u11_26274/12_2023/7u11_26274.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u11_26274/12_2023/7u11_26274.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u11_26274/12_2023/7u11_26274.pdb"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    2202      2.51       5
     N     531      2.21       5
     O     702      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 3456
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "B"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "C"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 3.78, per 1000 atoms: 1.09
  Number of scatterers: 3456
  At special positions: 0
  Unit cell: (106.326, 99.882, 32.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      21     16.00
     O     702      8.00
     N     531      7.00
     C    2202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 301 " - " ASN A 183 "
      " NAG A 302 " - " ASN A 151 "
      " NAG A 303 " - " ASN A 145 "
      " NAG A 304 " - " ASN A 164 "
      " NAG B 301 " - " ASN B 183 "
      " NAG B 302 " - " ASN B 151 "
      " NAG B 303 " - " ASN B 145 "
      " NAG B 304 " - " ASN B 164 "
      " NAG C 301 " - " ASN C 183 "
      " NAG C 302 " - " ASN C 151 "
      " NAG C 303 " - " ASN C 145 "
      " NAG C 304 " - " ASN C 164 "
  Time building additional restraints: 1.34
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  786

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 62.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 126
      removed outlier: 6.490A  pdb=" N   VAL A 123 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   ILE B 126 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   TYR A 125 " --> pdb=" O   ILE B 126 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   VAL B 123 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   ILE C 126 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   TYR B 125 " --> pdb=" O   ILE C 126 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 137
      removed outlier: 6.406A  pdb=" N   LYS A 129 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 8.195A  pdb=" N   TYR B 132 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 9.017A  pdb=" N   ALA A 131 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   SER B 134 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 9.064A  pdb=" N   VAL A 133 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 9.513A  pdb=" N   ASP B 136 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 8.674A  pdb=" N   TYR A 135 " --> pdb=" O   ASP B 136 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LYS B 129 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
      removed outlier: 8.223A  pdb=" N   TYR C 132 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 9.029A  pdb=" N   ALA B 131 " --> pdb=" O   TYR C 132 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   SER C 134 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
      removed outlier: 9.054A  pdb=" N   VAL B 133 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
      removed outlier: 9.507A  pdb=" N   ASP C 136 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 8.663A  pdb=" N   TYR B 135 " --> pdb=" O   ASP C 136 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 165
      removed outlier: 6.354A  pdb=" N   ILE A 142 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
      removed outlier: 7.871A  pdb=" N   ASN B 145 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
      removed outlier: 8.827A  pdb=" N   LEU A 144 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   THR B 147 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 9.166A  pdb=" N   ILE A 146 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 10.094A  pdb=" N   THR B 149 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   ASN A 148 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 10.371A  pdb=" N   ASN B 151 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 9.000A  pdb=" N   LEU A 150 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 10.179A  pdb=" N   THR B 153 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 9.148A  pdb=" N   ILE A 152 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 9.738A  pdb=" N   ASN B 155 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 8.843A  pdb=" N   ASN A 154 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
      removed outlier: 10.221A  pdb=" N   TYR B 157 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
      removed outlier: 9.093A  pdb=" N   ASN A 156 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 10.310A  pdb=" N   SER B 159 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
      removed outlier: 9.344A  pdb=" N   TYR A 158 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 10.345A  pdb=" N   GLU B 161 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   VAL A 160 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
      removed outlier: 8.844A  pdb=" N   GLU B 163 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   VAL A 162 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   ILE B 165 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   ASN A 164 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ILE B 142 " --> pdb=" O   TYR C 143 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   ASN C 145 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 8.847A  pdb=" N   LEU B 144 " --> pdb=" O   ASN C 145 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   THR C 147 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 9.158A  pdb=" N   ILE B 146 " --> pdb=" O   THR C 147 " (cutoff:3.500A)
      removed outlier: 10.075A  pdb=" N   THR C 149 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
      removed outlier: 9.050A  pdb=" N   ASN B 148 " --> pdb=" O   THR C 149 " (cutoff:3.500A)
      removed outlier: 10.343A  pdb=" N   ASN C 151 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 8.961A  pdb=" N   LEU B 150 " --> pdb=" O   ASN C 151 " (cutoff:3.500A)
      removed outlier: 10.136A  pdb=" N   THR C 153 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 9.102A  pdb=" N   ILE B 152 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
      removed outlier: 9.685A  pdb=" N   ASN C 155 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 8.785A  pdb=" N   ASN B 154 " --> pdb=" O   ASN C 155 " (cutoff:3.500A)
      removed outlier: 10.164A  pdb=" N   TYR C 157 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      removed outlier: 9.031A  pdb=" N   ASN B 156 " --> pdb=" O   TYR C 157 " (cutoff:3.500A)
      removed outlier: 10.248A  pdb=" N   SER C 159 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
      removed outlier: 9.277A  pdb=" N   TYR B 158 " --> pdb=" O   SER C 159 " (cutoff:3.500A)
      removed outlier: 10.278A  pdb=" N   GLU C 161 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   VAL B 160 " --> pdb=" O   GLU C 161 " (cutoff:3.500A)
      removed outlier: 8.788A  pdb=" N   GLU C 163 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   VAL B 162 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
      removed outlier: 7.728A  pdb=" N   ILE C 165 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   ASN B 164 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 177
    Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181
      removed outlier: 6.589A  pdb=" N   ARG A 180 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ARG B 180 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 187
    Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198
      removed outlier: 6.797A  pdb=" N   ILE A 195 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ASP B 196 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   TYR A 197 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   THR B 198 " --> pdb=" O   TYR A 197 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ILE B 195 " --> pdb=" O   GLN C 194 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ASP C 196 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   TYR B 197 " --> pdb=" O   ASP C 196 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   THR C 198 " --> pdb=" O   TYR B 197 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 201 through 203
      removed outlier: 6.376A  pdb=" N   VAL A 202 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   VAL B 202 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 209 through 219
      removed outlier: 6.244A  pdb=" N   TYR A 209 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   ASP B 212 " --> pdb=" O   TYR A 209 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   TYR A 211 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   CYS B 214 " --> pdb=" O   TYR A 211 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   PHE A 213 " --> pdb=" O   CYS B 214 " (cutoff:3.500A)
      removed outlier: 10.393A  pdb=" N   LEU B 216 " --> pdb=" O   PHE A 213 " (cutoff:3.500A)
      removed outlier: 8.853A  pdb=" N   THR A 215 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
      removed outlier: 9.814A  pdb=" N   SER B 218 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
      removed outlier: 8.806A  pdb=" N   ILE A 217 " --> pdb=" O   SER B 218 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   TYR B 209 " --> pdb=" O   MET C 210 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   ASP C 212 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   TYR B 211 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   CYS C 214 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 8.397A  pdb=" N   PHE B 213 " --> pdb=" O   CYS C 214 " (cutoff:3.500A)
      removed outlier: 10.416A  pdb=" N   LEU C 216 " --> pdb=" O   PHE B 213 " (cutoff:3.500A)
      removed outlier: 8.878A  pdb=" N   THR B 215 " --> pdb=" O   LEU C 216 " (cutoff:3.500A)
      removed outlier: 9.832A  pdb=" N   SER C 218 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
      removed outlier: 8.833A  pdb=" N   ILE B 217 " --> pdb=" O   SER C 218 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 224 through 228
    Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245
      removed outlier: 6.593A  pdb=" N   THR A 234 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   PHE B 237 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   TYR A 236 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   HIS B 239 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   GLY A 238 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 8.447A  pdb=" N   GLU B 241 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   SER A 240 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 8.321A  pdb=" N   ILE B 243 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   GLN A 242 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   GLN B 245 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   SER A 244 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   THR B 234 " --> pdb=" O   THR C 235 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   PHE C 237 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   TYR B 236 " --> pdb=" O   PHE C 237 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   HIS C 239 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   GLY B 238 " --> pdb=" O   HIS C 239 " (cutoff:3.500A)
      removed outlier: 8.430A  pdb=" N   GLU C 241 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   SER B 240 " --> pdb=" O   GLU C 241 " (cutoff:3.500A)
      removed outlier: 8.318A  pdb=" N   ILE C 243 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   GLN B 242 " --> pdb=" O   ILE C 243 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   GLN C 245 " --> pdb=" O   GLN B 242 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   SER B 244 " --> pdb=" O   GLN C 245 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 251 through 253

    40 hydrogen bonds defined for protein.
    120 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.80

  Time building geometry restraints manager: 1.42 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 1053
        1.34 -     1.46: 810
        1.46 -     1.58: 1617
        1.58 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 3516
  Sorted by residual:
  bond pdb=" C1  NAG A 304 "
       pdb=" O5  NAG A 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.39e+01
  bond pdb=" C1  NAG C 304 "
       pdb=" O5  NAG C 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.37e+01
  bond pdb=" C1  NAG B 304 "
       pdb=" O5  NAG B 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" CG  LEU B 226 "
       pdb=" CD2 LEU B 226 "
    ideal  model  delta    sigma   weight residual
    1.521  1.427  0.094 3.30e-02 9.18e+02 8.09e+00
  bond pdb=" CG  LEU C 226 "
       pdb=" CD2 LEU C 226 "
    ideal  model  delta    sigma   weight residual
    1.521  1.427  0.094 3.30e-02 9.18e+02 8.09e+00
  ... (remaining 3511 not shown)

  Histogram of bond angle deviations from ideal:
      100.08 -   106.41: 58
      106.41 -   112.74: 1983
      112.74 -   119.06: 875
      119.06 -   125.39: 1860
      125.39 -   131.72: 12
  Bond angle restraints: 4788
  Sorted by residual:
  angle pdb=" N   THR B 231 "
        pdb=" CA  THR B 231 "
        pdb=" C   THR B 231 "
      ideal   model   delta    sigma   weight residual
     108.34  111.85   -3.51 1.31e+00 5.83e-01 7.18e+00
  angle pdb=" N   THR A 231 "
        pdb=" CA  THR A 231 "
        pdb=" C   THR A 231 "
      ideal   model   delta    sigma   weight residual
     108.34  111.84   -3.50 1.31e+00 5.83e-01 7.12e+00
  angle pdb=" N   THR C 231 "
        pdb=" CA  THR C 231 "
        pdb=" C   THR C 231 "
      ideal   model   delta    sigma   weight residual
     108.34  111.78   -3.44 1.31e+00 5.83e-01 6.90e+00
  angle pdb=" CA  TYR A 158 "
        pdb=" CB  TYR A 158 "
        pdb=" CG  TYR A 158 "
      ideal   model   delta    sigma   weight residual
     113.90  118.60   -4.70 1.80e+00 3.09e-01 6.82e+00
  angle pdb=" CA  TYR C 158 "
        pdb=" CB  TYR C 158 "
        pdb=" CG  TYR C 158 "
      ideal   model   delta    sigma   weight residual
     113.90  118.60   -4.70 1.80e+00 3.09e-01 6.81e+00
  ... (remaining 4783 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.42: 2067
       24.42 -    48.84: 168
       48.84 -    73.26: 24
       73.26 -    97.68: 3
       97.68 -   122.10: 9
  Dihedral angle restraints: 2271
    sinusoidal: 1038
      harmonic: 1233
  Sorted by residual:
  dihedral pdb=" CB  CYS C 214 "
           pdb=" SG  CYS C 214 "
           pdb=" SG  CYS C 253 "
           pdb=" CB  CYS C 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  140.13  -47.13     1      1.00e+01 1.00e-02 3.07e+01
  dihedral pdb=" CB  CYS B 214 "
           pdb=" SG  CYS B 214 "
           pdb=" SG  CYS B 253 "
           pdb=" CB  CYS B 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  140.13  -47.13     1      1.00e+01 1.00e-02 3.07e+01
  dihedral pdb=" CB  CYS A 214 "
           pdb=" SG  CYS A 214 "
           pdb=" SG  CYS A 253 "
           pdb=" CB  CYS A 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  140.09  -47.09     1      1.00e+01 1.00e-02 3.06e+01
  ... (remaining 2268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 486
       0.071 -    0.142: 111
       0.142 -    0.213: 3
       0.213 -    0.285: 0
       0.285 -    0.356: 6
  Chirality restraints: 606
  Sorted by residual:
  chirality pdb=" C1  NAG C 301 "
            pdb=" ND2 ASN C 183 "
            pdb=" C2  NAG C 301 "
            pdb=" O5  NAG C 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.04   -0.36 2.00e-01 2.50e+01 3.16e+00
  chirality pdb=" C1  NAG B 301 "
            pdb=" ND2 ASN B 183 "
            pdb=" C2  NAG B 301 "
            pdb=" O5  NAG B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.04   -0.36 2.00e-01 2.50e+01 3.16e+00
  chirality pdb=" C1  NAG A 301 "
            pdb=" ND2 ASN A 183 "
            pdb=" C2  NAG A 301 "
            pdb=" O5  NAG A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.14e+00
  ... (remaining 603 not shown)

  Planarity restraints: 591
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 199 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.62e+00
        pdb=" N   PRO A 200 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 200 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 200 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 199 "   -0.026 5.00e-02 4.00e+02   4.02e-02 2.59e+00
        pdb=" N   PRO C 200 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO C 200 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C 200 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 199 "   -0.026 5.00e-02 4.00e+02   4.02e-02 2.58e+00
        pdb=" N   PRO B 200 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 200 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 200 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 588 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 99
        2.73 -     3.27: 3252
        3.27 -     3.81: 5670
        3.81 -     4.36: 6339
        4.36 -     4.90: 12507
  Nonbonded interactions: 27867
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 161 "
            pdb=" ND1 HIS A 239 "
     model   vdw
     2.186 2.520
  nonbonded pdb=" OE2 GLU B 161 "
            pdb=" ND1 HIS B 239 "
     model   vdw
     2.186 2.520
  nonbonded pdb=" OE2 GLU C 161 "
            pdb=" ND1 HIS C 239 "
     model   vdw
     2.187 2.520
  nonbonded pdb=" NZ  LYS B 129 "
            pdb=" OD2 ASP B 136 "
     model   vdw
     2.316 2.520
  nonbonded pdb=" NZ  LYS A 129 "
            pdb=" OD2 ASP A 136 "
     model   vdw
     2.317 2.520
  ... (remaining 27862 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ 
ugh 304))
  selection = (chain 'B' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ 
ugh 304))
  selection = (chain 'C' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ 
ugh 304))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             2.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          9.040
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     15.980
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6126
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.094   3516  Z= 0.352
  Angle     :  0.731   5.930   4788  Z= 0.381
  Chirality :  0.062   0.356    606
  Planarity :  0.004   0.040    579
  Dihedral  : 17.788 122.100   1476
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  1.57 %
    Favored  : 96.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS C 222 
   PHE   0.007   0.001   PHE B 237 
   TYR   0.017   0.002   TYR B 143 
   ARG   0.001   0.000   ARG B 140 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.370 
Fit side-chains
  outliers start: 9
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1447
  time to fit residues: 7.3712
Evaluate side-chains
  24 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.341 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.5627
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6360
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3516  Z= 0.301
  Angle     :  0.764   7.195   4788  Z= 0.387
  Chirality :  0.059   0.327    606
  Planarity :  0.004   0.028    579
  Dihedral  : 16.571 113.944    711
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  7.35 %
    Favored  : 91.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 222 
   PHE   0.013   0.003   PHE B 171 
   TYR   0.022   0.003   TYR A 143 
   ARG   0.004   0.001   ARG A 180 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 35
  average time/residue: 0.0934
  time to fit residues: 4.7772
Evaluate side-chains
  30 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.364 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0350
  time to fit residues: 0.7232
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 35 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0060
   chunk 12 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.9802

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6399
moved from start:          0.3644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3516  Z= 0.259
  Angle     :  0.723   8.568   4788  Z= 0.366
  Chirality :  0.057   0.314    606
  Planarity :  0.003   0.019    579
  Dihedral  : 15.863 112.703    711
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  9.45 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 239 
   PHE   0.012   0.003   PHE B 171 
   TYR   0.020   0.002   TYR A 143 
   ARG   0.002   0.000   ARG B 180 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 35
  average time/residue: 0.1267
  time to fit residues: 6.0020
Evaluate side-chains
  32 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.371 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0470
  time to fit residues: 0.8965
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0050
   chunk 0 optimal weight:    8.9990
   overall best weight:    2.4002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 168 GLN
B 168 GLN
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6485
moved from start:          0.4578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3516  Z= 0.305
  Angle     :  0.785  10.705   4788  Z= 0.399
  Chirality :  0.060   0.371    606
  Planarity :  0.004   0.022    579
  Dihedral  : 16.371 112.646    711
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 13.65 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.17 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 239 
   PHE   0.014   0.002   PHE B 171 
   TYR   0.024   0.003   TYR A 143 
   ARG   0.002   0.001   ARG B 180 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 28
  average time/residue: 0.1028
  time to fit residues: 4.2836
Evaluate side-chains
  29 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.371 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0443
  time to fit residues: 0.6740
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 15 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0050
   chunk 0 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.0798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6391
moved from start:          0.4731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3516  Z= 0.169
  Angle     :  0.644   7.500   4788  Z= 0.323
  Chirality :  0.055   0.269    606
  Planarity :  0.003   0.028    579
  Dihedral  : 14.967 109.507    711
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 13.65 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 239 
   PHE   0.008   0.001   PHE B 171 
   TYR   0.017   0.001   TYR A 143 
   ARG   0.001   0.000   ARG A 180 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 30
  average time/residue: 0.1271
  time to fit residues: 5.2455
Evaluate side-chains
  30 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.356 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0420
  time to fit residues: 0.6538
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
B 155 ASN
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 155 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6584
moved from start:          0.5863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   3516  Z= 0.425
  Angle     :  0.875   7.872   4788  Z= 0.452
  Chirality :  0.064   0.432    606
  Planarity :  0.004   0.030    579
  Dihedral  : 17.397 113.201    711
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 15.22 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.44 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.62 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS A 239 
   PHE   0.018   0.003   PHE B 171 
   TYR   0.028   0.004   TYR C 143 
   ARG   0.003   0.001   ARG A 140 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 30
  average time/residue: 0.1172
  time to fit residues: 4.9444
Evaluate side-chains
  27 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.363 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0332
  time to fit residues: 0.5739
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
moved from start:          0.6217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   3516  Z= 0.317
  Angle     :  0.788   9.382   4788  Z= 0.408
  Chirality :  0.060   0.371    606
  Planarity :  0.004   0.036    579
  Dihedral  : 16.195 109.288    711
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 17.59 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.51 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 239 
   PHE   0.015   0.003   PHE B 171 
   TYR   0.025   0.003   TYR A 143 
   ARG   0.002   0.001   ARG B 180 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1576
  time to fit residues: 6.6359
Evaluate side-chains
  27 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.366 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.5278
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 155 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6507
moved from start:          0.6331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3516  Z= 0.212
  Angle     :  0.685   7.749   4788  Z= 0.352
  Chirality :  0.057   0.304    606
  Planarity :  0.003   0.044    579
  Dihedral  : 15.339 108.140    711
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 17.59 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 239 
   PHE   0.010   0.002   PHE A 171 
   TYR   0.018   0.002   TYR A 143 
   ARG   0.001   0.000   ARG B 140 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 33
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 33
  average time/residue: 0.1423
  time to fit residues: 6.2044
Evaluate side-chains
  31 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.328 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4747
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   overall best weight:    1.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6540
moved from start:          0.6662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3516  Z= 0.236
  Angle     :  0.713   7.914   4788  Z= 0.367
  Chirality :  0.058   0.342    606
  Planarity :  0.004   0.049    579
  Dihedral  : 15.577 109.187    711
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 17.32 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.40 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS B 239 
   PHE   0.010   0.002   PHE A 171 
   TYR   0.020   0.002   TYR A 143 
   ARG   0.002   0.000   ARG B 140 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 30
  average time/residue: 0.1129
  time to fit residues: 4.8328
Evaluate side-chains
  32 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.372 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0357
  time to fit residues: 0.6516
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6563
moved from start:          0.6879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3516  Z= 0.268
  Angle     :  0.739   8.649   4788  Z= 0.380
  Chirality :  0.060   0.356    606
  Planarity :  0.004   0.053    579
  Dihedral  : 15.536 108.409    711
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 17.32 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.47 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS B 239 
   PHE   0.012   0.002   PHE A 171 
   TYR   0.022   0.002   TYR A 143 
   ARG   0.002   0.000   ARG B 140 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 34
  average time/residue: 0.1233
  time to fit residues: 5.7097
Evaluate side-chains
  32 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.376 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0406
  time to fit residues: 0.6203
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4930 r_free = 0.4930 target = 0.182399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.156576 restraints weight = 9080.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.4671 rms_B_bonded: 3.83
r_work: 0.4516 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.4516
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4499
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4499 r_free = 0.4499    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4500 r_free = 0.4500    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4500
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6592
moved from start:          0.6992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3516  Z= 0.266
  Angle     :  0.741   8.198   4788  Z= 0.381
  Chirality :  0.060   0.410    606
  Planarity :  0.004   0.057    579
  Dihedral  : 15.772 111.053    711
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 17.85 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.45 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.62 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS B 239 
   PHE   0.013   0.002   PHE A 171 
   TYR   0.021   0.002   TYR A 143 
   ARG   0.002   0.000   ARG B 140 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1191.27 seconds
wall clock time: 22 minutes 36.97 seconds (1356.97 seconds total)